I've been having this same problem on a recurring basis. I look up and the iPhone Cellular Calls option is mysteriously unchecked on my Mac. Trying to turn it back on results in the "FaceTime and iCloud must be signed in to the same Apple ID to use iPhone Cellular Calls." error message. So this is what gets it working for me again. At least temporarily.
Note: I am running OS X Yosemite 10.10.3 Public Beta. iOS 8.3 Public Beta. And I have Two-Step Authentication turned on my Apple ID.
1. Log out of FaceTime on my iPhone.
2. Log out of FaceTime on my Mac.
3. Log out of iMessage on my Mac.
4. Attempt to log in to FaceTime on my Mac with my regular Apple ID password. I get the message that I need an "app-specific password". Click Create which takes me to the Apple website in Safari. I log in to my Apple ID account. Receive the code on my iPhone. Enter that code in Safari on my Mac. Receive a prompt that asks me to create an "app-specific password" for BOTH FaceTime and iMessage. <--- This is important! Create the "app-specific password".
5. Enter the "app-specific password" when logging in to FaceTime on my iPhone. Make sure your Apple ID is checked in "You can be reached for FaceTime at:." Turn on iPhone Cellular Calls if it is not already selected.
6. Enter the "app-specific password" when logging in to FaceTime on my Mac. Make sure your Apple ID is checked in "You can be reached for FaceTime at:."
7. Enter the "app-specific password" when logging in to iMessage on my Mac. Make sure your Apple ID is checked in "You can be reached for messages at:."
8. Reboot my Mac. iPhone Cellular Calls is then selected in FaceTime on my Mac.
I think the key here is that FaceTime on both the Mac and iPhone along with iMessage on the Mac need to all be "playing in the same sandbox" by being logged in with the same Apple ID and "app-specific password". For some reason iMessage on the iPhone doesn't have its own login separate from iCloud so there is no "app-specific password" to enter in that instance. As I stated at the beginning ... this seems to work temporarily. Hopefully Apple will have all this sorted out by the time the final release of OS X Yosemite 10.10.3 and iOS 8.3 come out.